Mitochondrial DNA diseases are highly complex and heterogeneous in both genotype and expression. This proposal is aimed at improving the accuracy and feasibility of diagnosing diseases of the mitochondrial DNA. In Phase I a DNA chip will be developed to resequence the entire 16.6 kb mitochondrial genome at single base resolution. This will allow the genome to be rapidly and completely screened for mutations. The ability to identify actual base changes will allow the potential impact of mutations to be assessed at the level of amino acid coding changes, or in terms of tRNA and rRNA structural changes. The feasibility of a 2 color detection system for quantitating mixtures of wild type and mutant DNA and a method for directly labeling unamplified mitochondrial DNA will be explored. In Phase II, a comprehensive reference database of mitochondrial sequences will be generated, and used in assessing the potential significance of sequence changes. In collaboration with other researchers, previously characterized clinical samples bearing known mutations will be reanalyzed to screen for secondary mutations or significant polymorphisms. Finally, the chip will be used to analyze unknown sequences, to further characterize performance and to identify new associations between sequence changes and disease. PROPOSED COMMERCIAL APPLICATION: DNA forensics. Rapid and improved genetic diagnosis for a phenotypically complex and diverse group of diseases.